5CQ1

Disproportionating enzyme 1 from Arabidopsis - cycloamylose soak


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X1N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82931 microliter of 9% PEG2000 MME in 0.1 M HEPES-NaOH, pH 8.0 was added to 1 microliter of protein at a concentration of 10 mg/ml in 20 mM HEPES-NaOH, pH 7.5, 150 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.6253

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.89α = 65.28
b = 73.35β = 69.49
c = 79.39γ = 66.86
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2011-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9173DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.332.02892.40.0770.0850.03714.35.3527395273941
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3692.20.5520.5520.2641.45.33900

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1X1N2.332.02850050268892.440.17720.17580.2051RANDOM41.1
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
2.091.351.22-1.32-1.680.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.853
r_dihedral_angle_3_deg14.394
r_dihedral_angle_4_deg14.18
r_dihedral_angle_1_deg5.941
r_mcangle_it1.896
r_angle_refined_deg1.394
r_mcbond_it1.179
r_mcbond_other1.175
r_angle_other_deg0.918
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.853
r_dihedral_angle_3_deg14.394
r_dihedral_angle_4_deg14.18
r_dihedral_angle_1_deg5.941
r_mcangle_it1.896
r_angle_refined_deg1.394
r_mcbond_it1.179
r_mcbond_other1.175
r_angle_other_deg0.918
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7968
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms120

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction